Merge branch 'development' into feature/ci-tests

4 files changed, 196 insertions, 0 deletions

diff --git a/src/extract_lambda.py b/src/extract_lambda.py
new file mode 100644
index 0000000..56b47a6
--- /dev/null
+++ b/src/extract_lambda.py
@@ -0,0 +1,144 @@
+from pg8000.native import Connection, DatabaseError, InterfaceError
+from dotenv import dotenv_values
+import boto3
+import csv
+from botocore.exceptions import ClientError
+import logging
+import json
+from datetime import datetime
+
+
+logger = logging.getLogger()
+logger.setLevel(logging.INFO)
+
+
+class DBConnectionException(Exception):
+    """Wraps pg8000.native Error or DatabaseError."""
+
+    def __init__(self, e):
+        """Initialise with provided error message."""
+        self.message = str(e)
+        super().__init__(self.message)
+
+def lambda_handler(event, context):
+    """This lambda function connects to the Totesys database, lists the contents of the ingestion bucket,
+       and converts all tables to CSV and if any of those tables do not exist in, or are different to the ones in s3, it uploads them
+       it uses 3 helper functions to achieve these 3 functionalities 
+    """
+    try:
+        db = connect_to_database()
+        existing_files = list_existing_s3_files()
+        any_changes = process_and_upload_tables(db, existing_files)
+        
+        if not any_changes:
+            logger.info("No changes detected in the database.")
+            return {
+                'statusCode': 200,
+                'body': json.dumps('No changes detected, no CSV files were uploaded.')
+            }
+        else:
+            return {
+                'statusCode': 200,
+                'body': json.dumps('CSV files processed and uploaded successfully.')
+            }
+        
+    except Exception as e:
+        logger.error(f'Error: {e}')
+        return {
+            'statusCode': 500,
+            'body': json.dumps('Internal server error.')
+        }
+    
+    finally:
+ 
+        if db:
+            db.close()
+
+def get_config(path: str = ".env") -> dict:
+    return dotenv_values(path)
+
+
+def connect_to_database() -> Connection:
+    try:
+        config = get_config()
+        host = config["host"]
+        port = config["port"]
+        user = config["user"]
+        password = config["password"]
+        database = config["database"]
+
+        return Connection(
+            database=database,
+            user=user,
+            password=password,
+            host=host,
+            port=port
+        )
+    except InterfaceError as i:
+        logger.error(f'Interface error: {i}')
+        raise DBConnectionException("Failed to connect to database")
+
+
+
+def list_existing_s3_files(bucket_name='extract_bucket', client=boto3.client('s3')):
+    """Creates a dictionary and populates it with the 
+       results of listing the contents of the s3 bucket, then
+       returns the populated dictionary
+    """
+    
+    existing_files = {}
+    
+    try:
+        response = client.list_objects_v2(Bucket='extract_bucket')
+        
+        if 'Contents' in response:
+            for obj in response['Contents']:
+                s3_key = obj['Key']
+                try:
+                    file_obj = client.get_object(Bucket=bucket_name, Key=s3_key)
+                    file_content = file_obj['Body'].read().decode('utf-8')
+                    existing_files[s3_key] = file_content
+                except ClientError as e:
+                    logger.error(f'Error retrieving S3 object {s3_key}: {e}')
+        else:
+            logger.error('The bucket is empty')
+    
+    except ClientError as e:
+        logger.error(f'Error listing S3 objects: {e}')
+    
+    return existing_files
+
+
+
+def process_and_upload_tables(db, existing_files, client=boto3.client('s3')):
+    """Creates a list of the tables from a database query and 
+       then selects everything from each table in individual queries
+       it then writes each table to CSV files and compares with the item 
+       in the existing_files dictionary with the same name. If it finds any changes
+       to files, or new tables/files it uploads them to the s3 bucket
+    """
+    
+    tables = db.run("SELECT table_name FROM information_schema.tables WHERE table_schema='public' AND table_type='BASE TABLE';")
+    
+    for table in tables:
+        table_name = table[0]
+        rows = db.run(f"SELECT * FROM {table_name};")
+        
+
+        csv_file_path = f"/tmp/{table_name}.csv"
+        with open(csv_file_path, "w", newline='') as file:
+            writer = csv.writer(file)
+            column_names = [desc["name"] for desc in db.columns(f"SELECT * FROM {table_name};")]
+            writer.writerow(column_names)
+            writer.writerows(rows)
+        
+        s3_key = f"{table_name}/{datetime.today().year}/{datetime.today().month}/{datetime.today().day}/{table_name}_{datetime.now().strftime('%H:%M:%S')}.csv"
+        new_csv_content = open(csv_file_path, "r").read()
+        
+
+        if s3_key not in existing_files or existing_files[s3_key] != new_csv_content:
+            try:
+                client.upload_file(csv_file_path, 'extract_bucket', s3_key)
+                logger.info(f"Uploaded {s3_key} to S3.")
+            except ClientError as e:
+                logger.error(f'Error uploading to S3: {e}')
\ No newline at end of file
diff --git a/src/load_lambda.py b/src/load_lambda.py
new file mode 100644
index 0000000..6ee681f
--- /dev/null
+++ b/src/load_lambda.py
@@ -0,0 +1,2 @@
+def lambda_handler():
+    pass
\ No newline at end of file
diff --git a/src/secrets_manager.py b/src/secrets_manager.py
new file mode 100644
index 0000000..c0fb61e
--- /dev/null
+++ b/src/secrets_manager.py
@@ -0,0 +1,48 @@
+import boto3
+from botocore.exceptions import ClientError
+import json
+
+
+def sm_client():
+    sm_client = boto3.client('secretsmanager')
+    yield sm_client
+
+def create_secret(sm_client, secret_name, cohort_id, user, password, host, database, port):
+    secret = {
+        "cohort_id": cohort_id,
+        "user": user,
+        "password": password,
+        "host": host,
+        "database": database,
+        "port": port
+    }
+
+    response = sm_client.create_secret(
+        Name = secret_name,
+        SecretString = json.dumps(secret)
+    )
+
+    print(response)
+    return response
+
+def list_secret(sm_client):
+    response = sm_client.list_secrets()
+    secret_dict = response['SecretList']
+    secret_names = []
+    for items in secret_dict:
+        secret_names.append(items['Name'])
+    print(f'{len(secret_names)} secret(s) available')
+    for name in secret_names:
+        print(name)
+    return secret_names
+
+def retrieve_secrets(sm_client):
+    response = sm_client.get_secrets(
+        
+    )
+
+
+
+#retrieve secret
+#so lambda can access totesy db
+#so lambda connect to the db and then retrieve the data
\ No newline at end of file
diff --git a/src/transform_lambda.py b/src/transform_lambda.py
new file mode 100644
index 0000000..6ee681f
--- /dev/null
+++ b/src/transform_lambda.py
@@ -0,0 +1,2 @@
+def lambda_handler():
+    pass
\ No newline at end of file